Unlockable weapons:
Unlock the following weapons by performing the corresponding tasks:

Bandanna - Complete a single-player session without killing anyone (including bosses). You can do this on any difficulty
Desert Eagle, Long Barrel - Earn the fox emblem on a single-player session
Digital Camera - In the nomad vehicle during the mission intermission; you can unlock a special photo by picking up this item in stage 4 instead of earlier
Patriot Future Assault Weapon - Earn the big boss emblem on a single-player session
Race (Ricochet) Gun - Clear the single-player game once
Rail Gun - Beat crying wolf
Scanning Plug S - Log more than 10 hours of metal gear online play time on the same profile as your metal gear 4 game. You purchase this from drebin.
Solar Gun - Collect the five statues (those of the 4 battle beauties and the frog soldier/haven troopers in stage 1) using non-lethal means on their respective idols
Stealth Item - Complete a single-player session without instigating a single alert (caution is okay, but not alert). You can do this on any difficulty.
Thor 45-70 - Earn the fox hound emblem on a single-player session
World War I Pistol - Earn the hound emblem on a single-player session

Unlockable emblems:
Unlock the following emblems by performing the corresponding tasks:

Ant Emblem - Shake 50 enemies for items.
Assassin's Emblem - Beat the game with 50+ knife kills, 50+ CQC holds, and 25 or less alerts.
Bear Emblem - Choke 100 enemies to death
Bee Emblem - Use the scanning plug S or syringe on 50 enemies
Big Boss Emblem - Beat the game on the highest difficulty with no deaths, no alerts, no kills, no recovery items, no stealth suit, no bandanna items, in under 5 hours.
Blue Bird Emblem - Give friendly soldiers 50 items
Centipede - Get less than 75 alert phases, less than 250 kills, and over 25 continues.
Chicken - Get over 150 alert phases, over 500 kills, over 50 continues, use over 50 recovery items and finish the game in over 35 hours.
Cow - Activate over 100 alerts
Crocodile - Have over 400 kills
Eagle Emblem - Get 150 headshots
Fox Emblem - Beat the game on normal or higher w/ no deaths, 5 or less alerts, no kills, no recovery items, no stealth suit, no bandanna items, in under 6 hours.
Fox Hound Emblem - Beat the game on hard or higher w/ no deaths, 3 or less alerts, no kills, no recovery items, no stealth suit, no bandanna items, in under 5.5 hours.
Frog Emblem - Dive or roll 200 times
Gecko Emblem - Press against walls for a total of 1 hour
Giant Panda Emblem - Complete the game after 30 cumulative hours of play
Gibbon Emblem - Hold up 50 enemies
Hawk Emblem - Be admired by 25 friendly soldiers
Hog Emblem - Get 10 combat highs
Hound Emblem - Beat the game on hard or higher w/ no deaths, 3 or less alerts, no kills, no recovery items, no stealth suit, no bandanna items, in under 6.5 hours.
Hyena Emblem - Pick up 400 dropped weapons
Inch Worm Emblem - Crawl on the ground for a total of 1 hour
Jaguar - Get over 75 alert phases, less than 250 kills, and less than 25 continues.
Leopard - Get over 75 alert phases, less than 250 kills, and over 25 continues.
Little Gray Emblem - Collect all 69 weapons
Lobster Emblem - Spend a total of 2.5 hours crouching
Mantis - Finish the game with no alerts activated, no continues, no rations, noodles or regains used and in under 5 hours
Octopus - Beat the game without activating any alert phases.
Panther - Get over 75 alert phases, over 250 kills, and less than 25 coninues.
Pig - Use more than 50 recovery items
Pigeon - Beat the game without killing a single person.
Puma - Get over 75 alert phases, over 250 kills, and over 25 continues.
Rabbit Emblem - Look at 100 playboy pages
Raven - Beat the game in under 5 hours
Scarab - Perform over 100 rolls
Scorpion - Get less than 75 alert phases, less than 250 kills, and less than 25 continues.
Spider - Get less than 75 alert phases, over 250 kills, and over 25 continues.
Tarantula - Get less than 75 alert phases, over 250 kills, and less than 25 continues.
Tortoise - Spend more than 60 minutes inside the drum can or card board box (this can be done throughout the game, not all at once)
Wolf - Beat the game with no continues and no rations, regains, or noodles used

Unlockable costumes:
Unlock the following costumes by performing the corresponding tasks:

Altair from Assassin's Creed costume - Get the assassin's emblem.
Civilian clothes - Start the eastern europe level.
Infinite Ammo Bandana - Complete the game without killing any enemies. It can also be purchased from drebin.
5,000,000 DP - Complete the game.
Opitcal Camo - Complete the game without going into alert phase. It can also be purchased from drebin for 5,000,000 DP after completing the game.
Middle East Militia Disguise - Go to the middle east militia safe house.
South American Militia Disguise - Go to the south american cove valley village.
Suit - Complete the game.

PMC troops ignore you:
Wear Otacon's or one of the beauty's face paints to be ignored by PMC soldiers.

Infinite Drebin points:
When in Shadow Moses, there will be respawning Dwarf Gekkos. Go to an area where they cannot reach you such as a vent. Continuously shoot at them(preferably with machine gun) to gain DP.

Statue locations:
Find the following statues in the corresponding locations. The statues are required to unlock the Solar gun. You must defeat the boss non-lethally. Stand in the sunlight to reload the solar gun.

Alternate ending:
An alternate ending will play if you are using the Sixaxis controller.

Custcene secrets:
Perform the following actions during the specified cutscenes to get the corresponding effects:

Naomi's Chest - In Act 2, when Snake loses his Psyche after Namoi tells him how long he has, press L1 to look at her chest. This will recharge Snake's Psyche.

Naomi Upskirt - In Act 2, when Snake drops his cigarette, use the hidden L1 option to look up Naomi's skirt.

Psycho Mantis' Ghost - In the first intermission sequence with Beauty and the Beast, after you use the option to look through L1, look to the left to see the ghost of Psycho Mantis.

Sorrow - In the Psycho Mantis intermission sequence, hold down L1. Psycho Mantis disappears and you will hear Sorrow say something. Hold L1 to see Sorrow. Press X to flashback.

Weird person tailing Snake:
When tailing the Resistance member look behind Snake, and occasionally you will see a man with a hat and trenchcoat tailing him. If you try to shoot him he will duck away around the corner and disappear.

Shake Rose's breasts:
To make Rose's breasts move, shake the Sixaxis controller when you speak to her on the codec.